diff --git a/renv/activate.R b/renv/activate.R index d13f993..90b251c 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.0.7" + version <- "1.1.4" attr(version, "sha") <- NULL # the project directory @@ -42,7 +42,7 @@ local({ return(FALSE) # next, check environment variables - # TODO: prefer using the configuration one in the future + # prefer using the configuration one in the future envvars <- c( "RENV_CONFIG_AUTOLOADER_ENABLED", "RENV_AUTOLOADER_ENABLED", @@ -98,6 +98,66 @@ local({ unloadNamespace("renv") # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + `%||%` <- function(x, y) { if (is.null(x)) y else x } @@ -142,12 +202,11 @@ local({ # compute common indent indent <- regexpr("[^[:space:]]", lines) common <- min(setdiff(indent, -1L)) - leave - paste(substring(lines, common), collapse = "\n") + text <- paste(substring(lines, common), collapse = "\n") - } + # substitute in ANSI links for executable renv code + ansify(text) - startswith <- function(string, prefix) { - substring(string, 1, nchar(prefix)) == prefix } bootstrap <- function(version, library) { @@ -305,8 +364,11 @@ local({ quiet = TRUE ) - if ("headers" %in% names(formals(utils::download.file))) - args$headers <- renv_bootstrap_download_custom_headers(url) + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } do.call(utils::download.file, args) @@ -385,10 +447,21 @@ local({ for (type in types) { for (repos in renv_bootstrap_repos()) { + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + # retrieve package database db <- tryCatch( as.data.frame( - utils::available.packages(type = type, repos = repos), + do.call(utils::available.packages, args), stringsAsFactors = FALSE ), error = identity @@ -470,6 +543,14 @@ local({ } + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + renv_bootstrap_download_github <- function(version) { enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") @@ -477,16 +558,19 @@ local({ return(FALSE) # prepare download options - pat <- Sys.getenv("GITHUB_PAT") - if (nzchar(Sys.which("curl")) && nzchar(pat)) { + token <- renv_bootstrap_github_token() + if (is.null(token)) + token <- "" + + if (nzchar(Sys.which("curl")) && nzchar(token)) { fmt <- "--location --fail --header \"Authorization: token %s\"" - extra <- sprintf(fmt, pat) + extra <- sprintf(fmt, token) saved <- options("download.file.method", "download.file.extra") options(download.file.method = "curl", download.file.extra = extra) on.exit(do.call(base::options, saved), add = TRUE) - } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { fmt <- "--header=\"Authorization: token %s\"" - extra <- sprintf(fmt, pat) + extra <- sprintf(fmt, token) saved <- options("download.file.method", "download.file.extra") options(download.file.method = "wget", download.file.extra = extra) on.exit(do.call(base::options, saved), add = TRUE) @@ -611,11 +695,19 @@ local({ } - renv_bootstrap_platform_prefix <- function() { + renv_bootstrap_platform_prefix_default <- function() { - # construct version prefix - version <- paste(R.version$major, R.version$minor, sep = ".") - prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + # read version component + version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") + + # expand placeholders + placeholders <- list( + list("%v", format(getRversion()[1, 1:2])), + list("%V", format(getRversion()[1, 1:3])) + ) + + for (placeholder in placeholders) + version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) # include SVN revision for development versions of R # (to avoid sharing platform-specific artefacts with released versions of R) @@ -624,10 +716,19 @@ local({ identical(R.version[["nickname"]], "Unsuffered Consequences") if (devel) - prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + version <- paste(version, R.version[["svn rev"]], sep = "-r") + + version + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- renv_bootstrap_platform_prefix_default() # build list of path components - components <- c(prefix, R.version$platform) + components <- c(version, R.version$platform) # include prefix if provided by user prefix <- renv_bootstrap_platform_prefix_impl() @@ -866,8 +967,14 @@ local({ } renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] - is.character(expected) && startswith(expected, version) + if (!is.character(expected)) + return(FALSE) + + pattern <- sprintf("^\\Q%s\\E", version) + grepl(pattern, expected, perl = TRUE) + } renv_bootstrap_validate_version_release <- function(version, description) { @@ -1047,10 +1154,10 @@ local({ renv_bootstrap_exec <- function(project, libpath, version) { if (!renv_bootstrap_load(project, libpath, version)) - renv_bootstrap_run(version, libpath) + renv_bootstrap_run(project, libpath, version) } - renv_bootstrap_run <- function(version, libpath) { + renv_bootstrap_run <- function(project, libpath, version) { # perform bootstrap bootstrap(version, libpath) @@ -1061,7 +1168,7 @@ local({ # try again to load if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { - return(renv::load(project = getwd())) + return(renv::load(project = project)) } # failed to download or load renv; warn the user @@ -1107,98 +1214,105 @@ local({ jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } - renv_json_read_default <- function(file = NULL, text = NULL) { + renv_json_read_patterns <- function() { - # find strings in the JSON - text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") - pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' - locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + list( - # if any are found, replace them with placeholders - replaced <- text - strings <- character() - replacements <- character() + # objects + list("{", "\t\n\tobject(\t\n\t", TRUE), + list("}", "\t\n\t)\t\n\t", TRUE), - if (!identical(c(locs), -1L)) { + # arrays + list("[", "\t\n\tarray(\t\n\t", TRUE), + list("]", "\n\t\n)\n\t\n", TRUE), - # get the string values - starts <- locs - ends <- locs + attr(locs, "match.length") - 1L - strings <- substring(text, starts, ends) + # maps + list(":", "\t\n\t=\t\n\t", TRUE), - # only keep those requiring escaping - strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + # newlines + list("\\u000a", "\n", FALSE) - # compute replacements - replacements <- sprintf('"\032%i\032"', seq_along(strings)) + ) - # replace the strings - mapply(function(string, replacement) { - replaced <<- sub(string, replacement, replaced, fixed = TRUE) - }, strings, replacements) + } - } + renv_json_read_envir <- function() { - # transform the JSON into something the R parser understands - transformed <- replaced - transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) - transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) - transformed <- gsub("[]}]", ")", transformed, perl = TRUE) - transformed <- gsub(":", "=", transformed, fixed = TRUE) - text <- paste(transformed, collapse = "\n") + envir <- new.env(parent = emptyenv()) - # parse it - json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + envir[["+"]] <- `+` + envir[["-"]] <- `-` - # construct map between source strings, replaced strings - map <- as.character(parse(text = strings)) - names(map) <- as.character(parse(text = replacements)) + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result + } - # convert to list - map <- as.list(map) + envir[["array"]] <- list - # remap strings in object - remapped <- renv_json_read_remap(json, map) + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL - # evaluate - eval(remapped, envir = baseenv()) + envir } - renv_json_read_remap <- function(json, map) { + renv_json_read_remap <- function(object, patterns) { - # fix names - if (!is.null(names(json))) { - lhs <- match(names(json), names(map), nomatch = 0L) - rhs <- match(names(map), names(json), nomatch = 0L) - names(json)[rhs] <- map[lhs] - } + # repair names if necessary + if (!is.null(names(object))) { + + nms <- names(object) + for (pattern in patterns) + nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) + names(object) <- nms - # fix values - if (is.character(json)) - return(map[[json]] %||% json) - - # handle true, false, null - if (is.name(json)) { - text <- as.character(json) - if (text == "true") - return(TRUE) - else if (text == "false") - return(FALSE) - else if (text == "null") - return(NULL) } - # recurse - if (is.recursive(json)) { - for (i in seq_along(json)) { - json[i] <- list(renv_json_read_remap(json[[i]], map)) - } + # repair strings if necessary + if (is.character(object)) { + for (pattern in patterns) + object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) } - json + # recurse for other objects + if (is.recursive(object)) + for (i in seq_along(object)) + object[i] <- list(renv_json_read_remap(object[[i]], patterns)) + + # return remapped object + object } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # read json text + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + + # convert into something the R parser will understand + patterns <- renv_json_read_patterns() + transformed <- text + for (pattern in patterns) + transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) + + # parse it + rfile <- tempfile("renv-json-", fileext = ".R") + on.exit(unlink(rfile), add = TRUE) + writeLines(transformed, con = rfile) + json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] + + # evaluate in safe environment + result <- eval(json, envir = renv_json_read_envir()) + + # fix up strings if necessary -- do so only with reversible patterns + patterns <- Filter(function(pattern) pattern[[3L]], patterns) + renv_json_read_remap(result, patterns) + + } + # load the renv profile, if any renv_bootstrap_profile_load(project) diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index e51d8dd..7517173 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.4.1", + "Version": "4.4.3", "Repositories": [ { "Name": "carpentries", @@ -17,326 +17,58 @@ ] }, "Packages": { - "R6": { - "Package": "R6", - "Version": "2.5.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" - ], - "Hash": "470851b6d5d0ac559e9d01bb352b4021" - }, - "base64enc": { - "Package": "base64enc", - "Version": "0.1-3", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" - ], - "Hash": "543776ae6848fde2f48ff3816d0628bc" - }, - "bslib": { - "Package": "bslib", - "Version": "0.8.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "base64enc", - "cachem", - "fastmap", - "grDevices", - "htmltools", - "jquerylib", - "jsonlite", - "lifecycle", - "memoise", - "mime", - "rlang", - "sass" - ], - "Hash": "b299c6741ca9746fb227debcb0f9fb6c" - }, - "cachem": { - "Package": "cachem", - "Version": "1.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "fastmap", - "rlang" - ], - "Hash": "cd9a672193789068eb5a2aad65a0dedf" - }, - "cli": { - "Package": "cli", - "Version": "3.6.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "b21916dd77a27642b447374a5d30ecf3" - }, - "digest": { - "Package": "digest", - "Version": "0.6.36", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "fd6824ad91ede64151e93af67df6376b" - }, - "evaluate": { - "Package": "evaluate", - "Version": "0.24.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "a1066cbc05caee9a4bf6d90f194ff4da" - }, - "fastmap": { - "Package": "fastmap", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" - }, - "fontawesome": { - "Package": "fontawesome", - "Version": "0.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "htmltools", - "rlang" - ], - "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" - }, - "fs": { - "Package": "fs", - "Version": "1.6.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a" - }, - "glue": { - "Package": "glue", - "Version": "1.7.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "e0b3a53876554bd45879e596cdb10a52" - }, - "highr": { - "Package": "highr", - "Version": "0.11", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "xfun" - ], - "Hash": "d65ba49117ca223614f71b60d85b8ab7" - }, - "htmltools": { - "Package": "htmltools", - "Version": "0.5.8.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "base64enc", - "digest", - "fastmap", - "grDevices", - "rlang", - "utils" - ], - "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" - }, - "jquerylib": { - "Package": "jquerylib", - "Version": "0.1.4", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "htmltools" - ], - "Hash": "5aab57a3bd297eee1c1d862735972182" - }, - "jsonlite": { - "Package": "jsonlite", - "Version": "1.8.8", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "methods" - ], - "Hash": "e1b9c55281c5adc4dd113652d9e26768" - }, - "knitr": { - "Package": "knitr", - "Version": "1.48", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "evaluate", - "highr", - "methods", - "tools", - "xfun", - "yaml" - ], - "Hash": "acf380f300c721da9fde7df115a5f86f" - }, - "lifecycle": { - "Package": "lifecycle", - "Version": "1.0.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "rlang" - ], - "Hash": "b8552d117e1b808b09a832f589b79035" - }, - "memoise": { - "Package": "memoise", - "Version": "2.0.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "cachem", - "rlang" - ], - "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" - }, - "mime": { - "Package": "mime", - "Version": "0.12", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "tools" - ], - "Hash": "18e9c28c1d3ca1560ce30658b22ce104" - }, - "rappdirs": { - "Package": "rappdirs", - "Version": "0.3.3", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" - ], - "Hash": "5e3c5dc0b071b21fa128676560dbe94d" - }, "renv": { "Package": "renv", - "Version": "1.0.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "utils" - ], - "Hash": "397b7b2a265bc5a7a06852524dabae20" - }, - "rlang": { - "Package": "rlang", "Version": "1.1.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Type": "Package", + "Title": "Project Environments", + "Authors@R": "c( person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Hadley\", \"Wickham\", role = c(\"aut\"), email = \"hadley@rstudio.com\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.", + "License": "MIT + file LICENSE", + "URL": "https://rstudio.github.io/renv/, https://github.com/rstudio/renv", + "BugReports": "https://github.com/rstudio/renv/issues", + "Imports": [ "utils" ], - "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1" - }, - "rmarkdown": { - "Package": "rmarkdown", - "Version": "2.27", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bslib", - "evaluate", - "fontawesome", - "htmltools", - "jquerylib", + "Suggests": [ + "BiocManager", + "cli", + "compiler", + "covr", + "cpp11", + "devtools", + "gitcreds", "jsonlite", + "jsonvalidate", "knitr", - "methods", - "tinytex", - "tools", - "utils", - "xfun", - "yaml" - ], - "Hash": "27f9502e1cdbfa195f94e03b0f517484" - }, - "sass": { - "Package": "sass", - "Version": "0.4.9", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "miniUI", + "modules", + "packrat", + "pak", "R6", - "fs", - "htmltools", - "rappdirs", - "rlang" - ], - "Hash": "d53dbfddf695303ea4ad66f86e99b95d" - }, - "tinytex": { - "Package": "tinytex", - "Version": "0.52", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "xfun" - ], - "Hash": "cfbad971a71f0e27cec22e544a08bc3b" - }, - "xfun": { - "Package": "xfun", - "Version": "0.46", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "grDevices", - "stats", - "tools" - ], - "Hash": "00ce32f398db0415dde61abfef11300c" - }, - "yaml": { - "Package": "yaml", - "Version": "2.3.10", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "51dab85c6c98e50a18d7551e9d49f76c" + "remotes", + "reticulate", + "rmarkdown", + "rstudioapi", + "shiny", + "testthat", + "uuid", + "waldo", + "yaml", + "webfakes" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes", + "NeedsCompilation": "no", + "Author": "Kevin Ushey [aut, cre] (), Hadley Wickham [aut] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Kevin Ushey ", + "Repository": "CRAN" } } }